Designing new molecules in a web browser

Last year we discussed our research aimed at re-imagining molecule design to bring the best of 2D and 3D technologies together in a collaborative environment. The project, code-named TorchWeb, has progressed significantly and is now on the count down to a beta release, expected in the early summer of this year, with an initial release to follow in the autumn.

The web-based interface contains plugin windows with key information. Here, in addition to the ‘Editor’ and ‘3D viewer’ plugins I have: the ‘Designs’ plugin that shows all the molecules that I am currently working on; the ‘LogP’ plugin giving an atomistic breakdown of the calculated logP; the ‘Properties’ plugin showing mutiple physico-chemical properties; and the ‘Similarity search’ plugin that shows similar molecules from a chosen database.

The two central concepts of this new product remain unchanged:

  • Firstly, we want to create an environment where medicinal chemists can draw molecules in a 2D editor, have these automatically converted into a 3D model of how the new molecule would interact with their target, or compare to the molecules that they have made before. To do this we created a new algorithm to grow molecules in 3D which is applied to every change in the 2D molecule.

The 3D pose of the molecule is updated interactively as the molecule is sketched in the 2D window enabling immediate assessment of the potential interactions that could be made by the new molecule. All other plugins also update, giving live similarity searches and logP predictions.

  • Secondly, we recognize that medicinal chemistry designers often work in teams across multiple locations and time zones. Consequently, collaboration had to be central to the application. This has been achieved through session sharing – enabling multiple users to share and simultaneously interact with a design and work on them together.

Joining a shared session enables users to collaborate live on any design, updating the 3D pose and chemical properties as the molecule evolves.

We are working steadily to convert our initial prototype into a full product. Collaboration with selected customers has enabled us to capture detailed requirements and to transition the code base into a robust, secure environment suitable for on-premise installation or deployment in the cloud.

Features have not been ignored! The design application will be joined by a data analysis application that will combine eye catching plots and graphs with 3D protein active site analysis.

Once designed a molecule still has to be made. Here we have embarked on a partnership with Elixir Software’s chemTraX. Together we will provide real time understanding on the status of every molecule from design to analysis, so you only make the molecules that you need to reach your goal.

Want to be among the first to learn more?

Subscribe to our newsletter.